The biogeochemical silicon (Si) cycle in coastal areas is of vital importance due to its crucial role in fueling diatom production that accounts for over half of carbon sequestration globally. However, recent studies have pointed out that Si-limited primary production may commonly occur in coastal systems under increasing human pressures. Therefore, it is crucial to understand Si dynamics and its response to drastic environmental changes in coastal areas. In this study, we investigated spatial and seasonal distribution of biogenic Si (BSi) and dissolved Si (DSi) combined with the silicon isotope values (δ³⁰Si_DSi) in the Yellow River estuary and the Bohai Sea, a typical semi-enclosed shallow coastal area that is heavily populated. Over an annual cycle, BSi and DSi concentrations varied up to two orders of magnitude, from 0 to 4 µM and from 0.3 to 40 µM, respectively. This is associated with large variations of δ³⁰Si_DSi ranging from +0.5 ± 0.21‰ to 2.93 ± 0.13‰ (2sd), in which lighter δ³⁰Si_DSi values are found in spring (+0.5 ± 0.21‰ - +1.76 ± 0.18‰) in comparison to the heavier values ranging from +1.24 ± 0.11‰ to +2.93 ± 0.13‰ in other seasons. In addition, the δ³⁰Si_DSi values in the Yellow River estuary were generally lighter than the Bohai Sea. Such patterns could be attributed to strong water mixing in the estuary, while primary production is the main process that fractionates Si isotopes in the Bohai Sea. Our results show that part of the Bohai Sea is facing Si-limited primary production in addition to conventionally-known nitrogen and phosphorous. Our findings also highlight the potential role of submarine fresh groundwater discharge as an important source of nutrients during the dry season.