There are extremely limited data on the prevalence and quantification of human bocavirus (HBoV) genotypes in different environments, particularly for rivers and drinking water. Here we performed quantitative real-time PCR (qPCR) to investigate the presence and load of HBoV genotypes in Nile water, drinking water, and effluent of the activated sludge wastewater treatment facility in Giza, Egypt. The results revealed that the detection rate of HBoV was 95.8%  (23/24) and 29.2%  (14/48) in effluents of the wastewater treatment facility and Nile water samples, respectively. HBoV was not found in drinking water samples from the Giza governorate. The mean concentration values of human bocavirus genotype HBoV-1, HBoV-2/4 and HBoV-3 were 0.52 log₁₀ GC/L, 2.2 log₁₀ GC/L, 0.3 log₁₀ GC/L, respectively in HBoV-positive Nile water samples (n = 14), while in HBoV-positive effluent of wastewater samples (n = 23) were 0.77 log₁₀ GC/L, 2.3 log₁₀ GC/L, and 1.6 log₁₀ GC/L, respectively. The viral type had a significant impact on the prevalence of the virus in surface water as well as effluent samples. A seasonal pattern of HBoV subtypes was observed in surface water (P  = 0.0002), as the highest detection rate was found during winter. Furthermore, the discharge of the effluent with higher viral concentration into the water sources leads to viral contamination of these sources, which may be a probable source for human infections. This study is executed to fill a gap of knowledge concerning the quantification and genotyping of bocavirus in Nile water, and enrich the scientific literature body by providing data about HBoV in environmental samples.