Thanks to its landscape and climatic conditions, the Istrian peninsula has long been characterized by wetlands as well as permanent and temporary ponds that represent hotspots of biodiversity. The sediment of swamps and ponds represents one of the fundamental habitats which records long-term conditions and changes in such systems. Therefore, the study of the microbial community in sediments, which is the most numerous component of the benthos of ponds, can contribute to a better interpretation of the overall ecological state of the aforementioned water bodies, and with the quantification of fecal bacteria, it is possible to recognize and quantify the level of certain potential anthropogenic pressures on the ecosystems and propose further measures for the protection of these areas. The research was conducted during winter and summer at six different locations in southwestern Istria. The number of heterotrophic prokaryotes in the sediments was determined using an epifluorescence microscope, while the sanitary quality of the sediment was determined using the most probable number method. Based on the collected data, it can be concluded that the ecological condition of the analyzed sediments is of moderate quality, especially in water bodies in the immediate vicinity of human settlements. Thus, it is necessary to take appropriate measures to prevent the additional intake of nutrient salts, organic matter or pollutants from roads, so that the stability of the mentioned water bodies can be preserved in the long term.