Urbanization and climate change exacerbate cyanobacterial harmful algal blooms (CHABs), impacting water quality and ecosystem health. Cyanobacteria are key primary producers that can proliferate in nutrient-rich conditions and disrupt aquatic environments. While CHAB management traditionally focuses on abiotic factors, tropical biodiversity requires more complex approaches. Other microbial communities that coexist with blooms, such as bacteria and cyanophages, play critical roles in regulating cyanobacterial populations through exchanges of gases and organic/inorganic compounds, as well as the lytic/lysogenic cycles, affecting bloom dynamics, nutrient cycling, and carbon flows. Advances in molecular sequencing have highlighted intricate cyanobacterial-bacterial-viral interactions, underscoring the influence of microbial communities and cyanophages on bloom development, toxin production, and nutrient turnover. This chapter examines the interactions between microbiomes, viromes, and cyanobacterial blooms in tropical urban catchments, using Singapore as a case study to address knowledge gaps in tropical freshwater ecosystems. We also highlight how horizontal gene transfer via cyanophages could drive adaptive traits in bloom-forming cyanobacteria. The current gaps in ecological data, especially with the rise of smaller pico-cyanobacteria under climate change, necessitate improved monitoring technologies.