Mid-field natural ponds promote regional biodiversity, providing alternative habitats for many valuable animal species. The study’s objective was to determine the most important abiotic factors, including hydrochemical and morphometric parameters, affecting fish occurrence in natural, small water bodies on agricultural lands. The studies were conducted in nine randomly selected water bodies located in Poland (the North European Plain). Eleven species of fish were recorded in the waterbodies, with the most abundant being cyprinids (mainly crucian carp). Canonical correspondence analysis (CCA) showed that an increase in oxygenation, temperature, amount of macrophytes, and K concentration and a decrease in the concentration of phosphates, electrical conductivity (EC), Mg, and Cl is associated with the most beneficial living conditions for the most frequently occurring species in the studied water bodies—crucian carp and tench. Aside from the hydrochemical parameters of water in the natural ponds, the number of fish correlates with the basin area and the pond area, maximum depth, area of the buffer zone surrounding the water bodies, and the number of macrophytes. This last factor also has a significant influence on the species’ abundance in the water bodies. Fish occurrences in mid-field ponds and common knowledge on their important role in the environment require taking steps to provide fish protection.