<p>We investigated changes in sediment grain size, elemental (total organic C, TOC; total N, TN), isotopic (δ¹³C, δ¹⁵N), biochemical composition (proteins, carbohydrates, lipids, phytopigments), nutritional quality, potential degradation of sedimentary organic matter across a river-to-lagoon continuum before-after high (HRP) and low (LRP) rainfall periods. Both rainfalls relocated the coarser sediment fraction downstream in the river, whilst only the finer fraction reached the lagoon. The high swell associated to the storm preceding the LRP contributed to the seawater overwash over the outer lagoon, which masked the effects of the freshwater discharge. After the HRP, TOC and TN in the outer lagoon increased 5–6 times, whilst after the LRP both decreased 2–8 times in the whole lagoon. Rainfalls caused a δ¹³C enrichment (from −&#xa0;27.1 to −&#xa0;22.0 ‰) of the lagoon sediments and changes in the biogeochemistry of both river and lagoon sediments. After both rainfalls, time for the degradation of the biopolymeric C increased downstream the river (5–11 times) and in the outer lagoon (3 times). We conclude that the effects of rainfall-driven river runoff and their spatial extent towards the adjacent lagoon depend on the magnitude and duration of the rainfall, which differently alter sediment biogeochemistry.</p>