Background Seasonal meteorological variations influence the spread of infectious diseases. Wastewater surveillance helps understanding pathogen transmission dynamics, particularly in urban areas of climate-vulnerable countries like Bangladesh. Methods We analysed 54 weeks of wastewater surveillance, clinical surveillance, and meteorological data from Dhaka, Bangladesh. Samples from 11 sites were tested for Vibrio cholerae (V. cholerae), SARS-CoV-2, Salmonella enterica subspecies enterica serovar Typhi (S. Typhi), and Group A rotavirus. Diarrhoeal Disease Surveillance data were sourced from icddr,b, and meteorological data from the Bangladesh Meteorological Department. Regression models adjusted for site and time variations were used for statistical analysis. Results Proportion of confirmed cholera cases among the diarrhoeal disease surveillance recruits were highest during post-monsoon (coef: 2.53; 95 % CI: 0.41 to 4.67; p = 0.029). V. cholerae log10 concentrations in wastewater were positively associated with pre-monsoon (coef: 0.93; 95 % CI: 0.26 to 1.58; p = 0.010), while SARS-CoV-2 peaked during monsoon (coef: 1.85; 95 % CI: 0.96 to 2.73; p < 0.001). S. Typhi and rotavirus log10 concentrations showed negative associations with pre-monsoon (coef: −0.96; 95 % CI: −1.68 to −0.27; p = 0.011, and −0.84; 95 % CI: −1.17 to −0.50; p < 0.001, respectively). Temperature positively influenced log10 concentrations of V. cholerae (adj. coef: 0.09; 95 % CI: 0.02 to 0.15; p = 0.014) and SARS-CoV-2 (adj. coef: 0.19; 95 % CI: 0.10 to 0.27; p < 0.001), but negatively associated with rotavirus (adj. coef: −0.06; 95 % CI: −0.10 to −0.03; p < 0.001). Similar associations were found between pathogen-positive samples and temperature. Conclusion Our study shows that seasonal, and meteorological factors (particularly temperature) influence the patterns and abundance of pathogens in wastewater and help in understanding disease transmission across different weather patterns.