Organic amendment is an effective method to reclaim salt-affected soil. However, in coastal land with shallow saline groundwater, it is limited known about the mechanism of organic amendment on soil desalinization. Thus, to examine the effect of topsoil organic matter content on soil water/salt transport and distribution, two-year field observations in Bohai coastal land, North China, and soil column experiments simulating salt accumulation and salt leaching were conducted, respectively. There were different organic fertilizer amendment rates in 0–20 cm topsoil, 0% (CK), 50% (OA 0.5), and 100% (OA 1.0) (w/w) for soil column experiments. Field observation showed that after organic amendment (OA), the soil’s physical structure was improved, and less of the increase in topsoil salt content was observed, with more salt accumulated in deep soil layers during the dry season. In addition, OA greatly promoted salt leaching during the rainy seasons. The results of the soil column tests further indicated that OA treatments significantly inhibited soil evaporation, with less salt accumulated in the topsoil. Although there was no difference in soil water distribution between the CK and OA 0.5 treatment, the topsoil EC for the OA 0.5 treatment was significantly lower than that for CK. During soil water infiltration, the OA 0.5 and OA 1.0 treatments significantly increased the infiltration rates, enhanced the wetting front, and promoted salt leaching to deeper soil layers, compared with CK. The improvement of soil organic amounts could make the soil more self-resistant to the coastal salinization. The findings of this study provide some insights into soil water/salt regulation in heterogeneous soil masses and on the permanent management of coastal saline farmland.