The human–animal bond is beneficial for human health, but companion animals also pose a potential threat as vectors of zoonotic parasites, especially in urban areas where both human and dog densities are high. However, the knowledge about parasitic spillover in the urban environment is relatively scarce. The aim of the present study was to reveal which factors determine parasitic contamination in Estonian towns and provide up-to-date information about intestinal parasites of the Estonian dog population. In total, 657 samples of dog excrement was collected over one year of investigation from five towns in Estonia. Generalized linear mixed models were used to evaluate factors predicting infection risk in urban areas. In general, infection risk and intensity models predicted higher infection with endoparasites for small dogs in smaller towns, especially in apartment-house districts and in potential hazard zones. Helminth eggs and Giardia/Cystoisospora oocysts were detected in 64 samples, with an overall prevalence of 9.8%.