There is lack of useful information that provides thorough understanding of the extent and severity of soil problems in salt-affected coastal lowland rice areas and their effect on farmer productivity. Soil physicochemical characterization was conducted in eight coastal rice fields in Balayan, Batangas, Philippines with varying distances from a source of saltwater intrusion. Soil, plant, and water samples were collected and analyzed from August 2014 to April 2015. Key farmer interviews were conducted. Soil organic matter was high in the wet season (WS) until the dry season (DS). Levels of soil nitrogen and phosphorus (P) were high at the end of WS and DS, indicating residuals from fertilization, and higher in fields closer to the swamp. The cation exchange capacity and base saturation in all sites were high. Zinc levels were low and may be due to high soil P. Results showed mildly alkaline soil at pH 7.4–7.7 across seasons. Soil electrical conductivity was higher in fields closer to the swamp and highest at end of WS. High exchangeable sodium percentage (ESP) indicates the presence of a high proportion of sodium in all fields regardless of distance from the swamp and at mean= 17.68% is higher than the limit set for sodic soil (15% ESP). Rice yields were within the range of varietal potential, including salinity tolerant variety Salinas, except in the field closest to the swamp which may be related to high ESP and soil sodium levels. This coastal lowland rice agroecosystem is classified as productive and the soil relatively fertile but prone to salinity and sodicity through saltwater intrusion from nearby swamps. Continued monitoring must be done so that farmers may be advised on soil fertility status and appropriate management options to sustain productivity.