Norovirus, a leading cause of acute gastroenteritis, significantly impacts global health, especially in developing countries where foodborne and environmental transmission remain challenging. This study examines the occurrence and seasonality of norovirus genogroups I (GI) and II (GII), their inter-annual variation and the prevalence of pepper mild mottle virus (PMMoV) as a potential viral indicator in oysters. Oysters were collected from one coastal sampling area on the Perfume River estuary, Hue City, Vietnam—a region with a tropical climate and limited wastewater treatment—over a 31-month period from March 2019 to October 2021 (34 sampling events, 240 individual oysters). Quantitative polymerase chain reaction (qPCR) was used to analyse viral genomes. Norovirus GI (45.4%, 109/240) was detected at a significantly higher rate than GII (35.4%, 85/240; χ²(1) = 4.576, p = 0.032). No significant difference in detection was found between dry and wet seasons for either GI (F(1,19) = 1.474, p = 0.240) or GII (Welch’s F(1,11.7) = 0.248, p = 0.627). However, significant inter-annual differences in dry season detection were observed for both GI (F(2,13) = 7.102, p = 0.008) and GII (Welch’s F(2,7.7) = 32.653, p < 0.001), with markedly lower detection in 2020 that may be associated with COVID-19 restrictions rather than climate variability, as rainfall data analysis did not support a climatic explanation. PMMoV was consistently detected across seasons (95.0%, 228/240) but showed no significant correlation with norovirus GI (r = 0.272, p = 0.120) or GII (r = 0.150, p = 0.396), suggesting it may not be a reliable quantitative proxy for norovirus contamination in oysters in this tropical setting. These findings highlight the importance of continuous oyster-based viral surveillance and improved wastewater management to reduce health risks associated with shellfish consumption in tropical coastal regions.