Coastal salt marshes play a critical role in carbon sequestration but are increasingly vulnerable to limate-driven shifts in episodic event frequency and intensity of episodic events such as heavy rain, droughts, heatwaves, and storm surges. This study examines hydrological and biogeochemical conditions in two salt marshes in Nova Scotia: Rainbow Haven Beach and Rushton’s Beach. The objectives are to (1) investigate how short-term weather conditions influence porewater composition and greenhouse gas (GHG) fluxes, and (2) evaluate environmental drivers of CO₂ and CH₄ fluxes. At each site, two shallow monitoring wells were installed along salinity gradients, and hydraulic head, temperature, and conductivity were monitored continuously for up to one year. GHG fluxes were measured using dynamic chambers and a portable trace gas analyzer, and porewater pH, conductivity, dissolved oxygen, and redox potential were measured using a multiparameter probe. Sampling occurred during dry and wet periods, drought, offshore storm influence, and heat warning days. A total of 596 GHG flux measurements were collected across 25 sampling days. Most measurements occurred during dry conditions (n = 501), with additional sampling during light (n = 47), heavy (n = 24), and extreme (n = 24) rainfall events. At Rainbow Haven Beach, median net CO₂ uptake ranged from −4.6 µmol m⁻² s⁻¹ during dry conditions to −0.6 µmol m⁻² s⁻¹ during heavy rainfall, while Rushton’s Beach exhibited greater variability. Porewater conductivity ranged from 10 to 45 mS cm⁻¹ across marsh zones and showed stronger associations with carbon flux variability at Rushton’s Beach, reflecting site-specific hydrology.