Benthic macroinvertebrates are very important components of aquatic environments, and monitoring their population dynamics helps us understand the effects of environmental factors on ecosystems. This study aimed to determine the dynamics of benthic macroinvertebrate fauna in paddy fields in the Meriç–Ergene River Basin (Turkish Thrace region) by investigating some physicochemical environmental parameters that may affect its distribution. For this purpose, water and sediment samples were collected from paddy fields in the study area during the cultivation season, including spring, summer and autumn of 2016, taking into account the water resources that supply the rice fields (artesian water, the Meriç River, the Ergene River and Meriç–Ergene mixed water). A total of 47 taxa (on average 8953 individuals per m2 ) were identified at the study sites. Water samples were analyzed to determine water temperature, pH, conductivity, salinity, total dissolved solids, calcium, magnesium, total hardness, nitrite nitrogen, nitrate nitrogen, phosphate, sulfate, dissolved oxygen and pesticides, and sediment samples were analyzed to determine the content of some heavy metals, including Cd, Ni, Cu, and Mn. The biological risk index (mERM-Q) and the potential ecological risk index (RI) were applied to the data and a hypothetical ecological risk analysis was conducted using our data and data available in the literature to assess the ecological risk profile of the ecosystem based on benthic macroinvertebrates. To this end, environmental factors were grouped based on the literature as heavy metals (S1), nutrients (S2), other physicochemical parameters (S3) and pesticides (S4), while organisms were grouped as Oligochaeta, Chironomidae, Insecta and others based on the dynamics of benthic macroinvertebrates to assess pressure factors. As a result, pesticides (S4) were found to exert the strongest ecological pressure on benthic macroinvertebrate fauna in paddy fields in the Meriç–Ergene River Basin.