Nutrient fluxes with river runoff can largely determine the state of coastal water ecosystems. The Vilyuchinskaya and Avachinskaya Bays of Kamchatka Peninsula were surveyed on 4–5 July 2022, just after the peak of the spring–summer flood of the Vilyucha and Avacha Rivers associated with the snow melting in volcanic areas. Additionally, water sampling was performed in river water in December 2022, in the period of winter low water. A general undersaturation of CO2 of surface waters was observed in the Vilyuchinskaya and Avachinskaya Bays. Strong supersaturation of CO2 of the near-bottom waters was observed, due to microbial destruction of organic matter, especially in Avachinskaya Bay. This organic matter was formed as a result of photosynthesis in the water column, which subsequently gravitated to the bottom and concentrated in specific bottom depressions in the studied bays. In these depressions, black sediments were found, in which sulfate reduction occurred. The porewater of sediments had a very high concentration of organic carbon, dissolved and organic nitrogen, and phosphates, as well as CO2 partial pressure. The source of nutrients for the studied bays is tephra (volcanic suspended particles), which covers all the watersheds, including the soil and snow, as a result of volcanic activity in the study region. Based on the calculated nutrient fluxes in river runoff for the summer and winter seasons and the DIN/DIP ratios in river, sea, and pore waters, the causes of phytoplankton blooms, including the occurrence of red tides, are discussed. The maximum flux of nutrients and, accordingly, phytoplankton blooms should be expected in the years with the highest volcanic activity and high summer air temperatures, since the melting of nutrient-rich snow and ice will be maximum. This will determine the flux of nutrients in the river runoff of the Kamchatka Peninsula and contribute to phytoplankton blooms.