Nitrogen dynamics in soils depends on nitrogen-fixing and denitrificating microorganisms, and the dynamics have been sufficiently modeled based on homogeneous infiltration of soil water. However, precise assessment and utilization of nitrogen in soils require the understanding on the spatial distribution of microorganisms and soil water. For instance, heterogeneous water paths in soils could maintain some types of anaerobic microorganisms those cannot survive in homogeneously moistened soils, even if the average water content in the soil is quite low. In the present study, two-dimensional distributions of soil water, nitrogen-containing ions, and nitrogen-fixing/denitrificating microorganisms were analyzed to clarify the spatial distribution of microorganisms and its effect on nitrogen dynamics in heterogeneously moistened soils. Sterilized fine sand from Arid Land Research Center of Tottori University was used. Ten percent (w/w) of sludge compost was applied as a source of microorganisms and nutrients for sandy soil reclamation. The sludge-amended sand sample was packed into a sterilized polycarbonate Hele-Shaw cell (width: 180 mm, height: 200 mm, thickness: 20 mm). The initial water contents of the sand and compost were 0.33% and 66%, respectively. The wet compost was used in order to maintain microorganisms that cannot survive in air-dried composts. Forty-three gram of sterilized pure water was applied at the surface center of the packed sample in order to make partial flow in the soil. The average water content was increased by the application of water from 4.3% to 9.0%. The sample in a Hele-Shaw cell was incubated at 30°C for 1 week with 12 hour/day of lightening at 30000 lx. Each side of the Hele-Shaw cell was covered with aluminum foil for shading. Gas exchange was maintained by applying the air through a 0.2 µm-pore filter. During the incubation, two-dimensional distribution of water content of the sample was monitored with a non-invasive capacitance moisture-meter (Accuscan, Delmhorst Inc., NJ, US) at 1 cm of sampling interval. Incubated sample was taken from several locations by considering the distribution of water content. Extraction of DNA from the samples was made with PowerSoil DNA extraction kit (MO Bio Laboratories, Inc., CA, US). Extracted DNA was amplified by PCR with nifH or nirK primer sets. The PCR products were applied to polyacrylamide gel electrophoresis (PAGE) at 100 V for 160 min in 1X TAE. Nitrogen-containing ions extracted by shaking with five-folds of distilled water (w/w) for 1 hour were measured by the indophenol-blue method and (cadmium/copper reduction) diazotization method. The non-invasive capacitance moisture meter could measure the water content distribution in the Hele-Shaw cell. The moisture distribution expanded quickly within 30 min, but the wetted region gradually expanded for 1 week after the quick expansion. The wetted depths after 30 min and 1 week were 3.5 cm and 6.5 cm, respectively. The sharp tip of the wetted front after 30 min was broadened during the incubation. The half-width of wetted region after 1 week was 6.1 cm. Therefore, the final distribution of soil moisture was classified into a partial flow while the initial distribution was similar to an expanding finger flow. Sampling points from the Hele-Shaw cell for nitrogen-containing ions and microbial DNA were A (0.5 cm depth, 0 cm from the center), B (2.5 cm, 0 cm), C (5.5 cm, 0 cm), D (10.5 cm, 0 cm), E (0.5 cm, 2.5 cm), F (0.5 cm, 5.5 cm), G (0.5 cm, 7.5 cm), and H (2.5 cm, 5.5 cm). Water-soluble ammonium ion concentration was very low (<0.1 mg/L) at the surface center of the soil (A), although the other samples showed 3.4-11.3 mg/L of ammonium. A possible reason for the low ammonium in (A) is two-dimensional leaching of ammonium. Nitrate ion concentration was highest in (D). The final moisture distribution did not show any water supply to (D) and (G), but nitrate concentration were 7.2 mg/L in (D) and 2.1 mg/L in (G). Therefore, it was indicated that denitrification at the surface thin layer within (G) should not be excluded for nitrogen assessment. Nitrite concentration was lowest in (A) and was highest in (B), that showed steep gradient of nitrite concentration within the partial flow. The native-PAGE of nifH indicated the highest presence of nitrogen-fixing microorganisms in (H), while the lowest presence were indicated in (D) and (E). The nifH amplification in the present study was significant at low water content, therefore it was implied that some drought-tolerant nifH-containing microorganisms dominated in the soil. The moisture contents in (D) and (E) were markedly different, therefore the possible reasons for the low presence of nifH were the high moisture content in (D) and the high nitrate concentration in (E), respectively. No nirK band was found in (D) and (G), while clear bands of nirK were found in the other samples. Therefore, it was confirmed that denitrification could be enhanced by partial flow in the soil.