In response to global urbanization and economic development, urban surface water pollution has become a universal challenge and particularly affects densely populated megacities, and Dhaka is no exception. The discharge of 98% of untreated domestic sewage and massive volumes of industrial wastewater from over 7000 industries escalate surface water crises. This study investigates microbial and fecal contamination with particular emphasis on Cryptosporidium in surface water, known for causing waterborne diseases, such as cryptosporidiosis. Findings reveal high Cryptosporidium oocyst concentrations and fecal contamination in various water bodies in Dhaka City. Among the investigated water bodies, the Buriganga River exhibits the highest Cryptosporidium oocyst concentration (46%), while the Balu River, Turag River, Shitalakkhya River, Dhanmondi Lake, Gulshan Lake, Banani Lake, Ramna Lake, and Crescent Lake also present high levels of oocyst concentrations ranging from 21–40%. This study also calculated infection risks and found that the infection risk of swimming is highest during the wet season and is (3.9 ± 2.2 (95% CI: 3.0–5.0)) × 10−2 per swimming event, whereas it is approximately (2.4 ± 1.9 (95% CI: 1.6–3.3)) × 10−2 during the dry season. Annual diving risks are approximately (1.2 ± 0.6 (95% CI: 0.9–1.4)) × 10−2, indicating considerably high risks. Most of the sampling sites generally show significantly higher risks than other study areas like the Mymensingh and Kushtia Districts. In light of these results, we strongly recommend immediate measures to address water quality issues and mitigate the risks associated with Cryptosporidium contamination in Dhaka’s surface water.