Coastal marine organisms experience dynamic pH and dissolved oxygen (DO) conditions in their natural habitats, which may impact their susceptibility to long-term anthropogenic changes. Robust characterizations of all temporal scales of natural pH and DO fluctuations in different marine habitats are needed; however, appropriate time series of pH and DO are still scarce. We used multiyear (2008–2012), high-frequency (6 min) monitoring data to quantify diel, seasonal, and interannual scales of pH and DO variability in a productive, temperate tidal salt marsh (Flax Pond, Long Island, US). pH_NBS and DO showed strong and similar seasonal patterns, with average (minimum) conditions declining from 8.2 (8.1) and 12.5 (11.4) mg l⁻¹ at the end of winter to 7.6 (7.2) and 6.3 (2.8) mg l⁻¹ in late summer, respectively. Concomitantly, average diel fluctuations increased from 0.22 and 2.2 mg l⁻¹ (February) to 0.74 and 6.5 mg l⁻¹ (August), respectively. Diel patterns were modulated by tides and time of day, eliciting the most extreme minima when low tides aligned with the end of the night. Simultaneous in situ pCO₂ measurements showed striking fluctuations between ∼330 and ∼1,200 (early May), ∼2,200 (mid June), and ∼4,000 μatm (end of July) within single tidal cycles. These patterns also indicate that the marsh’s strong net heterotrophy influences its adjacent estuary by ‘outwelling’ acidified and hypoxic water during ebb tides. Our analyses emphasize the coupled and fluctuating nature of pH and DO conditions in productive coastal and estuarine environments, which have yet to be adequately represented by experiments.