Groundwater Science, Geochemistry and Data Analysis

Science beneath the surface

Water moves, even deep beneath the surface.

We share practical expertise in groundwater and geochemical modeling (MODFLOW, PHREEQC) for environmental and water resource assessment, along with data analysis using Python, AI, and Vibe Coding.
Exploring the world of water through science, code, and diverse perspectives—this is a platform to decipher natural phenomena from data.

SCIENCE · CODE · INSIGHT · WATER

Groundwater Geochemistry Hydrology AI & Python MODFLOW PHREEQC Geography Geothermal Science

About This Site

DeepFlows is a site run by a researcher specializing in groundwater science and geochemistry, dedicated to explaining the science and documenting the practice of data analysis. Rainwater seeps underground, flows slowly through aquifers, and eventually mixes with seawater along the coast. We decipher these "invisible movements of water," one step at a time, using numerical simulation and code.

This is not about memorizing textbook facts. From groundwater flow analysis with MODFLOW, to modeling water–rock chemical reactions with PHREEQC, to data visualization with Python, we explain the very methods used in real research—including the dead ends and the trial-and-error that rarely make it into published papers. The content is written for students learning hydrogeology, engineers in the water-resource and environmental fields, and anyone curious about numerical analysis and data science.

📘

Introduction to Groundwater Science

From core concepts—aquifers, hydraulic conductivity, recharge—to time-series analysis of freshwater lenses and tidal response. A 17-part series for learning systematically.

⚗️

PHREEQC Geochemical Modeling

From the basics of water-quality calculation to reaction-path modeling and inverse modeling. A 19-part series explaining geochemical simulation with real examples and code.

🗒️

Field Notes

Hot-spring water chemistry, the links between landforms and history, and the failures faced in everyday computation. Essays that don't fit the tutorial format.

Author: Heejun Yang, Ph.D.

A researcher specializing in hydrology, groundwater flow analysis, and geochemistry, with 26 peer-reviewed publications. Sharing the methods built up through years of research, in the plainest language possible. ＞ See full profile and publications

☀️ Featured Series

PHREEQC Tutorial

A complete guide to geochemical modeling, deciphering chemical reactions between water and rock. From installation to reaction path modeling.

READ IN ENGLISH > 日本語で読む >

Groundwater Science

Practical know-how for groundwater flow analysis and hydrothermal geochemical simulations using MODFLOW and FloPy.

READ IN ENGLISH > 日本語で読む >

Introduction to Groundwater Science #9: Diagnosing the Aquifer with the Tide — From Time Lag to Hydraulic Conductivity, and Back to the Water Level

The ocean tide is a natural signal generator for probing the ground. Using real observations from Minami-Daito Island, we derive the aquifer’s hydraulic conductivity from the tidal time lag and amplitude ratio — and then reconstruct the groundwater level itself with a lag-based multiple regression.

2026/07/10

DeepFlows

Introduction to Groundwater Science #8: Measuring the Time Lag — The Flood Pulse of Tonle Sap Lake and Cross-Correlation Analysis

In Southeast Asia’s largest lake, the river reverses its flow every rainy season. Using this ‘flood pulse’ as our case study, we introduce three tools of time-series analysis — auto-correlation, cross-correlation, and the cross-wavelet transform — to measure the hidden ‘time lag’ between two water-level signals.

2026/06/29

DeepFlows

Introduction to Groundwater Science #7: An Island Breathing with the Tide — The Freshwater Lens of Minami-Daito

On the remote uplifted atoll of Minami-Daito, a freshwater lens floats beneath the limestone. Using FFT and time-series analysis of real field data, we reveal how ocean tides shake the groundwater and how rainfall reshapes the lens.

2026/06/27

DeepFlows

Introduction to Groundwater Science #6: Time-Series Analysis & FFT — Relationship Between Unconfined Groundwater Level and Barometric Pressure

Analysis of the long-term decline of unconfined groundwater levels observed in southern Beppu. We discuss the interaction between hydrothermal and meteoric groundwater systems, geologic structures, and the hydrogeological significance of monitoring water levels.

2026/06/13

DeepFlows

Getting Started with PHREEQC #19: Specific Surface Area Pitfalls — Unit Mismatch and Physical Meaning of Calibration Factors

We explain the critical pitfalls of unit mismatch and missing molecular weight/initial mineral mass in PHREEQC surface area settings. We mathematically demonstrate how these errors corrupt the physical meaning of calibration parameters and propose a rigorous practice for transparent model reporting.

2026/06/11

DeepFlows

Getting Started with PHREEQC #18: Reproducing Basalt-CO2 Reactions and Introduction to Modeling Techniques — Satake et al. (2025)

Using the batch reaction experimental data from Satake et al. (2025), a Japanese CO2-EGS study, we explain the process of achieving perfect consistency between experimental values and models. This is done by applying practical modeling techniques not explicitly stated in the paper, such as interpreting units, introducing reactive surface area, and back-calculating initial values from bulk rock composition.

2026/06/10

DeepFlows

Getting Started with PHREEQC #17: Modeling Basalt-CO2 Reactions — Reproducing the CarbFix Project

Taking a step forward from the introduction to KINETICS, we use Gysi (2016) as a case study to implement and reproduce the complex simulation of basalt dissolution and secondary mineral precipitation in geologic CO2 sequestration (CarbFix) using PHREEQC.

2026/06/09

DeepFlows

Introduction to PHREEQC #16: Kinetics Basics — Tracking Calcite Dissolution Over Time

Moving beyond equilibrium calculations (‘what happens eventually?’), this article explores the dimension of time (‘how long does it take?’). We introduce the basics of Kinetics and demonstrate how to implement a simple Calcite dissolution model in PHREEQC.

2026/06/08

DeepFlows

Introduction to Groundwater Science #5: Where Does the River Water Come From? — Interaction Between River and Groundwater

Why doesn’t a river dry up even after weeks of no rain? This article explores how rivers and groundwater are connected, discussing hydraulic principles such as gaining/losing streams, kinematic/diffusion wave approximations, and Manning’s equation. We also implement the Lyne-Hollick digital filter in Python to perform hydrograph baseflow separation.

2026/06/07

Heejun Yang

Introduction to Groundwater Science #3: Why Does Groundwater Move? — Darcy’s Law and the Physics of Head

What is the driving force behind groundwater movement? Learn the concept of total head derived from Bernoulli’s theorem, the differences between saturated and unsaturated zones, the mechanics of unconfined and confined aquifers, and Darcy’s Law — the most fundamental law of groundwater flow — through a 1D model built with FloPy (MODFLOW 6).

2026/06/05

Heejun Yang