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MIKE SHE Public Data Catalog

Japan

Version: 0.1 test template
Purpose: Country-specific public dataset catalog for building simple to advanced MIKE SHE models
Region: Japan (Hokkaido, Honshu, Shikoku, Kyushu, Okinawa and other islands)

Quick Start

Minimum Public Datasets for Recharge Modelling with MIKE SHE (Japan)

If your objective is to calculate distributed groundwater recharge (without simulating groundwater flow or rivers), only five dataset categories are required.

The datasets below are free and cover the whole of Japan. Many portals are in Japanese only, and some require registration.

MIKE SHE Input Dataset Type Recommended Dataset Spatial Availability Why recommended
Topography (DEM) Gridded GSI Fundamental Geospatial Data – DEM (5 m where available, 10 m nationwide) Japan Official national DEM. The 5 m product is based on airborne LiDAR and photogrammetry and covers most plains and many mountain areas; the 10 m product covers the whole country.
Land Cover Gridded JAXA High-Resolution Land Use and Land Cover Map Japan 10 m land cover with Japan-specific classes, including paddy fields, cropland, deciduous and evergreen forest, bamboo and urban areas.
Soil Hydraulic Properties Vector Japan Soil Inventory (NARO) Japan National digital soil map (1:50,000 to 1:200,000) covering agricultural and forest soils, with soil profile descriptions. Van Genuchten parameters must be derived with pedotransfer functions.
Precipitation Gridded NARO Agro-Meteorological Grid Square Data for daily modelling

JMA Radar/Raingauge-Analyzed Precipitation (via DIAS) for sub-daily modelling		 Japan The NARO grid provides daily 1 km rainfall and other variables interpolated from AMeDAS. Radar/raingauge analysis provides 1 km, 30-minute rainfall for storm and flood events.
Time Series JMA historical weather data (AMeDAS)

MLIT Water Information System rain gauges		 Nationwide (~1,300 AMeDAS rain gauges plus MLIT gauges) One of the densest station networks in the world, with 10-minute to daily data. Can be used directly or to check gridded products.
Meteorological Forcing / Potential ET Gridded NARO Agro-Meteorological Grid Square Data Japan Daily 1 km temperature, humidity, solar radiation, wind and snow variables for calculating reference ET. No national PET grid exists, so FAO-56 reference ET must be calculated.
Time Series JMA historical weather data Nationwide Full meteorological observations at JMA observatories and AMeDAS sites for calculating reference ET within MIKE SHE.

Optional Improvements

Dataset Purpose
National Land Numerical Information (MLIT) Rivers, basins, lakes, dams, land-use meshes and many other national layers
MAFF field polygons Exact paddy and upland field boundaries
Vegetation map (Biodiversity Center of Japan) Detailed natural vegetation types
JAXA GCOM-C LAI (G-Portal) Dynamic Leaf Area Index (LAI)
AsiaFlux / JapanFlux Validation of actual evapotranspiration at flux sites
JAXA AMSR2 soil moisture (G-Portal) Regional soil-moisture validation
  1. Download the GSI 5 m DEM (or the 10 m DEM where 5 m is missing).
  2. Delineate the model domain and prepare the terrain model.
  3. Download the JAXA land-cover map and assign MIKE SHE vegetation classes, including paddy fields.
  4. Download the Japan Soil Inventory and derive soil hydraulic parameters.
  5. Choose your meteorological forcing:
  6. Option A (recommended): Use the NARO 1 km grid for daily forcing, supplemented by radar/raingauge-analyzed precipitation for events.
  7. Option B: Import AMeDAS observations directly into MIKE SHE.
  8. Let MIKE SHE calculate evapotranspiration and snowmelt internally using the selected vegetation and soil parameters.
  9. Represent flooded paddy fields during the irrigation season, as they are a major recharge source.
  10. Export the distributed groundwater recharge for use in MODFLOW, FEFLOW, or other groundwater models.

1. Introduction for advanced data sources

1.1 Purpose

This document summarizes public datasets that can be used to construct a physically based MIKE SHE model for Japan.

The catalog is organized according to the typical MIKE SHE model-building workflow rather than only by dataset type. It covers datasets for terrain, land cover, meteorological forcing, snow, ET, rivers, soils, hydrogeology, groundwater, water management, and calibration.

1.2 Intended Use

This catalog is intended for:

  • rapid screening models
  • river basin water-balance models
  • groundwater recharge and sustainable groundwater use studies
  • paddy-field and agricultural water management studies
  • flood and sediment studies
  • snowmelt studies
  • land subsidence assessments
  • applied MIKE SHE model setup

1.3 General Notes for Japan

  • Japanese public datasets are extensive but many portals and documentation are only in Japanese.
  • GSI data are generally available under terms compatible with CC BY 4.0. National Land Numerical Information datasets have individual terms; some restrict commercial use. JMA radar archives are distributed for a fee by the Japan Meteorological Business Support Center, but are available for research via DIAS.
  • The national datum is JGD2011. Models typically use the Japan Plane Rectangular Coordinate System (19 zones) or UTM zones 51–56. Elevations refer to T.P. (Tokyo Peil, mean sea level of Tokyo Bay).
  • Groundwater data are held mainly by prefectures and municipalities, not by a single national agency.

2. Hydrological Characteristics of Japan

2.1 Climate

  • humid temperate climate in most of Honshu, Shikoku and Kyushu
  • subarctic climate in Hokkaido
  • subtropical climate in Okinawa
  • Baiu rainy season (June–July) and typhoons (August–October)
  • heavy snowfall on the Sea of Japan side (Hokuriku, Tohoku, Hokkaido)
  • extreme short-duration rainfall from linear rainbands
  • annual rainfall mostly between 1,000 and 3,000 mm, locally above 4,000 mm

2.2 Topography

  • around 70% mountainous terrain
  • short, steep rivers with rapid flood response
  • alluvial plains and fans (e.g. Kanto, Nobi, Osaka, Niigata, Toyama plains)
  • numerous volcanoes with highly permeable deposits and large springs (e.g. Mt Fuji, Aso)
  • coastal lowlands, partly below sea level, protected by levees

2.3 Major Hydrological Challenges

  • flash floods, sediment disasters and extreme rainfall
  • historical land subsidence due to groundwater pumping (e.g. Tokyo, Osaka, Niigata)
  • groundwater use for snow melting on roads, lowering water tables in winter (e.g. Niigata, Hokuriku)
  • snowmelt contribution to river flow and recharge
  • paddy fields as a major source of groundwater recharge
  • sustainable groundwater management under the Basic Act on the Water Cycle
  • seawater intrusion on coasts and islands
  • earthquake impacts on groundwater systems

2.4 Major Aquifer Systems

  • Kanto Plain multi-layer aquifer system
  • Nobi Plain (Nagoya)
  • Osaka Plain
  • Kumamoto region (Aso pyroclastic deposits; water supply almost entirely from groundwater)
  • Mt Fuji volcanic aquifers and springs
  • Niigata Plain
  • alluvial fans of the Toyama Plain (e.g. Kurobe fan)
  • Tokachi and Ishikari plains (Hokkaido)
  • Ryukyu limestone aquifers with subsurface dams (e.g. Miyakojima)

3. Recommended Dataset Stack

Component Recommended Dataset Alternative Dataset Importance
DEM GSI 5 m DEM GSI 10 m DEM, AW3D30 ★★★★★
Land cover JAXA HRLULC NLNI land-use mesh ★★★★★
Paddy fields MAFF field polygons JAXA paddy class ★★★★★
Natural vegetation Vegetation map (Biodiversity Center) – ★★★★☆
LAI JAXA GCOM-C LAI MODIS MCD15A3H ★★★★☆
Precipitation NARO grid / JMA radar analysis (DIAS) AMeDAS, MLIT XRAIN ★★★★★
Climate forcing NARO grid AMeDAS, JRA-3Q ★★★★★
Potential ET FAO-56 from NARO grid AMeDAS ★★★★★
Snow JMA analyzed snow depth / NARO grid AMeDAS snow depth ★★★★★ (snow regions)
Rivers NLNI rivers GSI vector data ★★★★★
Lakes / dams NLNI lakes and dams MLIT Water Information System ★★★★☆
Soil Japan Soil Inventory SoilGrids ★★★★★
Geology Seamless Digital Geological Map (GSJ) GSJ Hydrogeological Environment Maps ★★★★★
Boreholes KuniJiban Geo-Station (NIED) ★★★★★
Groundwater heads Prefectures and municipalities MLIT Water Information System ★★★★★
Streamflow calibration MLIT Water Information System Prefectural gauges ★★★★★
Actual ET validation AsiaFlux / JapanFlux MODIS MOD16, GLEAM ★★★★☆
Soil moisture validation JAXA AMSR2 SMAP ★★★☆☆

4. Terrain Model

4.1 Purpose in MIKE SHE

Terrain data are required for model surface elevation, overland-flow gradients, surface storage, catchment delineation, river network verification, and floodplain connectivity.

4.2 Dataset Comparison

Dataset Coverage Resolution Format MIKE SHE Suitability Advantages Limitations Recommendation
GSI 5 m DEM Plains and many mountain areas 5 m XML (JPGIS/GML) Primary DEM LiDAR-based, bare-earth Not complete in all mountains; format conversion needed ★★★★★
GSI 10 m DEM Japan 10 m XML (JPGIS/GML) Gap filling, regional models Nationwide Derived from contours ★★★★☆
Prefectural LiDAR Selected prefectures (e.g. Shizuoka) ≤1 m Various Local models Very detailed, often open data Coverage varies ★★★★★ (where available)
AW3D30 Global 30 m GeoTIFF Backup Consistent Coarse ★★☆☆☆

4.3 Typical Preprocessing

  • convert GSI XML tiles to raster (free conversion tools are available)
  • merge 5 m and 10 m tiles
  • reproject to Plane Rectangular or UTM coordinates
  • burn in levees and drainage channels in lowlands
  • resample to model grid

4.4 Quality Checks

  • check levees and embankments in lowland plains
  • check paddy terraces in mountain valleys
  • check areas below sea level and pumping-station drainage in coastal lowlands
  • compare derived catchments with NLNI basin boundaries

5. Surface Water

5.1 Rivers

Dataset Coverage Format MIKE SHE / MIKE 1D Use Advantages Limitations Recommendation
NLNI rivers and basins Japan Vector River network, river codes, basins Official, with river classification Requires simplification ★★★★★
GSI vector data Japan Vector Water lines and water bodies Detailed Topology limited ★★★★☆
River cross-section surveys Class A rivers (MLIT) Survey data MIKE 1D cross-sections Detailed geometry Access by request ★★★★★

5.2 Lakes, Dams and Wetlands

Dataset Use Recommendation
NLNI lakes and dams Lake and dam locations and attributes ★★★★☆
MLIT Water Information System Dam inflow, release and storage ★★★★★
Vegetation map (Biodiversity Center) Wetland vegetation ★★★☆☆

5.3 Typical Preprocessing

  • simplify river network
  • include levees, weirs, dams and pumping stations
  • include agricultural canals and drainage networks in paddy areas
  • define river-bed conductance, especially on alluvial fans where rivers lose water
  • assign river and dam boundary conditions

6. Land Cover and Vegetation

6.1 Purpose in MIKE SHE

Land cover and vegetation define interception, ET parameters, root depth, crop coefficients, Manning roughness, irrigation zones (paddy fields), and impervious areas.

6.2 Dataset Comparison

Dataset Coverage Resolution Format MIKE SHE Use Advantages Limitations Recommendation
JAXA HRLULC Japan 10 m Raster Primary land-cover zones Japan-specific classes, including paddy Snapshot periods ★★★★★
NLNI land-use mesh Japan 100 m Raster / mesh Land-use time series Several years since 1976 Coarser ★★★★☆
MAFF field polygons Japan Field parcels Vector Paddy and upland fields Exact field boundaries Agriculture only ★★★★★
Vegetation map (Biodiversity Center) Japan 1:25,000 Vector Forest and natural vegetation types Very detailed Survey dates vary ★★★★☆

6.3 Vegetation Datasets

Parameter Dataset Use Recommendation
LAI JAXA GCOM-C / MODIS MCD15A3H Seasonal LAI (deciduous forest, crops) ★★★★☆
Crop coefficient FAO-56 and Japanese paddy studies Rice and upland crops ★★★★☆
Forest types Vegetation map Cedar and cypress plantations, broadleaf forest ★★★★☆

6.4 Typical Preprocessing

  • reclassify into MIKE SHE vegetation zones
  • separate paddy fields, upland crops, orchards, conifer plantations (sugi, hinoki), broadleaf forest, bamboo and urban areas
  • define paddy ponding periods, water depths and irrigation schedules
  • assign seasonal LAI to deciduous forest and crops

7. Meteorological Forcing

7.1 Precipitation

Dataset Coverage Resolution Temporal Resolution MIKE SHE Use Advantages Limitations Recommendation
NARO Agro-Meteorological Grid Japan 1 km Daily Long-term forcing High resolution, several variables Registration and use terms ★★★★★
JMA Radar/Raingauge-Analyzed Precipitation Japan 1 km 30 min Event and sub-daily forcing Radar merged with gauges Archive via JMBSC (fee) or DIAS (research) ★★★★★
MLIT XRAIN Major urban and river areas 250 m 1 min Urban flash floods Very high resolution Archive via DIAS ★★★★☆
AMeDAS Station network Point 10 min to daily Station forcing Dense, free Point data ★★★★★
JRA-3Q Global ~40 km 6-hourly Long-term context JMA reanalysis Coarse ★★☆☆☆

7.2 Climate Variables

Variable Recommended Dataset Alternatives MIKE SHE Use
Air temperature NARO grid AMeDAS ET, snow/rain distinction, snowmelt
Wind speed NARO grid AMeDAS Penman-Monteith
Humidity NARO grid JMA observatories Vapour-pressure deficit
Solar radiation NARO grid JMA observatories, sunshine duration ET energy term
Reference ET FAO-56 from NARO grid AMeDAS PET forcing

7.3 Snow

Snow is essential on the Sea of Japan side, in Hokkaido and in mountain areas.

Dataset Use Recommendation
JMA analyzed snow depth (~5 km) Gridded snow depth and snowfall ★★★★☆
AMeDAS snow depth Station snow depth ★★★★★
NARO grid snow variables Gridded snow model outputs ★★★★☆
MODIS Snow Cover Snow extent ★★★☆☆

8. Soil Data

8.1 Dataset Comparison

Dataset Coverage Resolution Parameters MIKE SHE Use Advantages Limitations Recommendation
Japan Soil Inventory (NARO) Japan 1:50,000 to 1:200,000 Soil types, profile descriptions Primary UZ zonation Official, includes forest soils Hydraulic parameters must be derived ★★★★★
Soil profile databases (NARO) Agricultural land Profiles Texture, bulk density, retention Parameter derivation Measured data Uneven coverage ★★★★☆
SoilGrids Global 250 m Texture, bulk density Backup Gridded Poor for andosols ★★☆☆☆

8.2 Typical Preprocessing

  • assign hydraulic parameters per soil group using pedotransfer functions and Japanese literature
  • treat andosols (volcanic ash soils) separately; they have very high porosity and water retention
  • represent the paddy plough pan as a low-conductivity layer
  • use thick, permeable forest soils in mountain catchments
  • calibrate against discharge, groundwater heads and snowmelt timing

9. Hydrogeology

9.1 Dataset Comparison

Dataset Coverage Use Advantages Limitations Recommendation
Seamless Digital Geological Map (GSJ, AIST) Japan Geological framework Nationwide 1:200,000 Hydrogeological interpretation required ★★★★★
GSJ Hydrogeological Environment Maps Selected regions Aquifer structure, groundwater levels, quality Hydrogeology-specific Selected areas only ★★★★★
KuniJiban (national borehole database) Japan Borehole logs from public works Many logs Mainly near infrastructure ★★★★★
Geo-Station (NIED) Japan Borehole and ground data Aggregates many sources Variable quality ★★★★☆
Prefectural groundwater surveys Prefectures Local aquifer models and reports Detailed Japanese only; by request ★★★★★

9.2 Conceptual Model Recommendations

  • multi-layer aquifers with aquitards in the large plains
  • compaction of clay layers and land subsidence
  • highly permeable alluvial fans with river losses
  • volcanic aquifers with large springs and long residence times
  • karst limestone aquifers on the Ryukyu Islands
  • seasonal recharge from flooded paddy fields
  • winter drawdown from snow-melting pumping

10. Groundwater Data

10.1 Heads and Monitoring Wells

Dataset Coverage Use Recommendation
Prefectural and municipal monitoring Local Heads and subsidence ★★★★★
MLIT Water Information System Selected wells Groundwater levels and quality ★★★★☆
Ministry of the Environment ground environment information Japan Subsidence and groundwater level overview ★★★★☆

10.2 Pumping and Water Use

Dataset Coverage Use Recommendation
Prefectural pumping reports and ordinances Local Registered pumping ★★★★☆
MLIT water resources white paper Japan National and regional water use statistics ★★★☆☆

11. Water Management

11.1 Relevant Processes

  • paddy irrigation with agricultural water rights
  • dams and river regulation
  • groundwater pumping for domestic, industrial and snow-melting use
  • managed recharge through winter flooding of paddy fields (e.g. Kumamoto)
  • subsurface dams on limestone islands
  • flood control, levees and drainage pumping stations

11.2 Regulatory Framework

  • the Basic Act on the Water Cycle (2014, amended 2021) promotes integrated water-cycle management, including groundwater management plans
  • the River Act governs river management and water rights
  • Class A rivers are managed by MLIT regional development bureaus; Class B rivers by prefectures
  • groundwater pumping is regulated by national laws in designated subsidence areas and by prefectural and municipal ordinances

11.3 Key Institutions

Topic Institution
Rivers, water resources, national land data MLIT
Geospatial data GSI
Meteorology JMA
Geology and hydrogeology Geological Survey of Japan (AIST)
Agriculture and soils MAFF, NARO
Satellite data JAXA
Research data archive DIAS

12. Remote Sensing Products

Dataset Coverage Resolution Use Recommendation
JAXA GCOM-C (SGLI) Global 250 m LAI, vegetation, snow ★★★★☆
JAXA GCOM-W (AMSR2) Global Coarse Soil moisture, snow ★★★☆☆
ALOS-2 PALSAR-2 Global 3–25 m Flood mapping, InSAR subsidence ★★★★☆
Sentinel-1 SAR / InSAR Global 10 m Flood mapping, subsidence ★★★★☆
Sentinel-2 Global 10 m Paddy flooding, crop calendars ★★★★☆
MODIS MOD16 Global 500 m Actual ET ★★★☆☆
GLEAM Global ~25 km Actual ET ★★☆☆☆
Himawari-8/9 (via JAXA) Asia-Pacific ~1–2 km Radiation, cloud, surface temperature ★★★☆☆

13. Calibration Datasets

Target Dataset Use Recommendation
River discharge MLIT Water Information System Streamflow calibration ★★★★★
Dam inflow MLIT Water Information System Upstream catchment calibration ★★★★★
Groundwater heads Prefectural and municipal monitoring SZ calibration ★★★★★
Spring discharge Local surveys Volcanic aquifer calibration ★★★★☆
Snow depth AMeDAS Snowmelt calibration ★★★★★
Actual ET AsiaFlux / JapanFlux ET validation ★★★★☆
Subsidence InSAR, levelling Compaction ★★★★☆

Recommended strategy: calibrate against discharge, groundwater heads and snow depth together, and include paddy irrigation seasons explicitly.

14. Typical MIKE SHE Workflow

  1. Define modelling objective and domain.
  2. Prepare the DEM from GSI 5 m and 10 m tiles.
  3. Build the river network from NLNI and MLIT survey data.
  4. Prepare land cover from JAXA HRLULC and MAFF field polygons.
  5. Assign vegetation parameters and paddy management schedules.
  6. Prepare precipitation from the NARO grid and radar/raingauge analysis.
  7. Prepare climate forcing, reference ET and snow inputs.
  8. Prepare soil properties from the Japan Soil Inventory.
  9. Build hydrogeological layers from GSJ maps and KuniJiban boreholes.
  10. Import groundwater heads and pumping from prefectural sources.
  11. Couple rivers, canals and groundwater.
  12. Calibrate discharge, heads and snow depth.
  13. Validate ET and subsidence.
  14. Document assumptions and uncertainties.

15. Minimum Dataset Package

Model Element Dataset
DEM GSI 10 m DEM
Land cover JAXA HRLULC
Precipitation NARO grid or AMeDAS
Climate forcing and PET NARO grid
Rivers NLNI rivers
Soils Japan Soil Inventory
Geology Seamless Geological Map
Streamflow MLIT Water Information System

16. Recommended Dataset Package

Model Element Dataset
DEM GSI 5 m DEM + prefectural LiDAR
Precipitation NARO grid + radar/raingauge analysis
Climate forcing and snow NARO grid + AMeDAS
Land cover JAXA HRLULC + MAFF field polygons + vegetation map
Soils Japan Soil Inventory + NARO profile data
Hydrogeology GSJ maps + KuniJiban boreholes
Groundwater heads and pumping Prefectures and municipalities
Discharge MLIT Water Information System
Actual ET AsiaFlux / JapanFlux

17. Premium Dataset Package

Dataset Type Possible Source Purpose
High-resolution LiDAR Prefectures, MLIT Detailed terrain and channels
River cross-sections MLIT regional bureaus Hydraulic modelling
XRAIN radar MLIT via DIAS Urban flash floods
Paddy water management records Land improvement districts Irrigation and recharge
Groundwater models and surveys Prefectures and municipalities Aquifer structure and parameters
Pumping tests Local surveys Hydraulic parameters
Isotope and age-tracer data Research institutes Recharge areas and residence times

18. Dataset Comparison Table Template

Dataset Coverage Spatial Resolution Temporal Resolution Time Period Format API / Access License MIKE SHE Use Advantages Limitations Recommendation
★☆☆☆☆

19. Data Preparation Checklist

Terrain

  • [ ] GSI DEM tiles downloaded and converted
  • [ ] DEM projected and clipped
  • [ ] levees and drainage checked

Surface Water

  • [ ] river network prepared
  • [ ] dams, weirs and pumping stations included
  • [ ] irrigation canals included where relevant

Land Cover and Vegetation

  • [ ] land cover reclassified
  • [ ] paddy fields identified from MAFF polygons
  • [ ] paddy ponding schedules defined
  • [ ] LAI assigned

Weather

  • [ ] NARO grid access registered
  • [ ] precipitation prepared
  • [ ] radar data obtained for events where needed
  • [ ] reference ET calculated
  • [ ] snow parameters defined

Soil

  • [ ] Japan Soil Inventory downloaded
  • [ ] hydraulic parameters assigned
  • [ ] andosols and plough pan represented

Groundwater

  • [ ] geology and boreholes collected
  • [ ] prefectural groundwater data requested
  • [ ] boundary conditions defined

Calibration and Validation

  • [ ] discharge and dam data obtained
  • [ ] groundwater heads obtained
  • [ ] snow depth data obtained
  • [ ] calibration periods defined

20. References and Official Data Portals

21. Notes on Uncertainty

  • extreme short-duration rainfall and its spatial variability
  • snow accumulation and melt in mountain areas
  • paddy-field water management and irrigation return flows
  • hydraulic parameters of andosols and volcanic deposits
  • groundwater pumping for snow melting and industry
  • aquitard compaction and subsidence
  • river-bed conductance on alluvial fans
  • dam and weir operations
  • aggregation from very fine datasets to model-grid resolution

A defensible model should document dataset choices, preprocessing assumptions, calibration strategy, validation results, and known limitations.

22. Regional Data Sources

River data for Class A rivers are held by MLIT regional development bureaus; groundwater data are held mainly by prefectures and municipalities.

Region MLIT Bureau Key Aquifers / Hydrological Focus
Hokkaido Hokkaido Regional Development Bureau Ishikari and Tokachi plains, snowmelt
Tohoku Tohoku Regional Development Bureau Snowmelt, Sendai Plain, post-2011 coastal changes
Kanto Kanto Regional Development Bureau Kanto Plain multi-layer aquifers, historical subsidence
Hokuriku Hokuriku Regional Development Bureau Niigata Plain, Toyama alluvial fans, snow-melting pumping
Chubu Chubu Regional Development Bureau Nobi Plain, Mt Fuji springs
Kinki Kinki Regional Development Bureau Osaka Plain, Lake Biwa
Chugoku Chugoku Regional Development Bureau Steep catchments, sediment disasters
Shikoku Shikoku Regional Development Bureau Water scarcity, reservoir-dependent supply
Kyushu Kyushu Regional Development Bureau Kumamoto groundwater and paddy recharge, Aso
Okinawa Okinawa General Bureau Ryukyu limestone aquifers, subsurface dams