Profiles and time-series of Oxygen, pH and CO2 was measured in situ in shallow (<10cm) tidal ponds located in the salt marshes of the Plum Island Estuary, MA, USA. The investigation was conducted using a novel needle optode profiling system from PreSens GmBH with an Automated Micromanipulator and needle-type optodes for measurements of oxygen (PM-PSt7), pH (PM-HP5), and CO2 (PM-CDM1 prototypes), respectively. The data provide novel information about the spatial and temporal variation of oxygen, pH and CO2 in water and sediment, driven by microphytobenthic photosynthesis and respiration. These parameters vary markedly throughout the day due to changes in light availability and temperature. The data characterizes salt marsh tidal ponds as a habitat with extreme oxygen dynamics. Data includes 1) In situ Oxygen, pH and CO2 profiles across the sediment-water interface in shallow salt marsh tidal ponds at 3 different times of the day; morning, afternoon and night, respectively; 2) Oxygen and pH profiles across the sediment-water interface under different light regimes; 0. 25, 150, 350 PAR (0 μmol photons m−2 s−1), respectively; 3) In situ time series of Oxygen, pH and temperature in shallow salt marsh tidal ponds.; 4) Oxygen profiles across the sediment-water interface in shallow salt marsh tidal ponds under different in situ light regimes, determined by a natural layer of seafoam covering the water surface.; 5) In situ oxygen profiles across the sediment-water interface in 3 different tidal ponds in the Plum Island Estuary.; 6) Oxygen profiles across the sediment-water interface in three different habitats in salt marshes: a) Tidal river; submerged sediment. b) Tidal ponds; submerged sediment and c) Vegetated marsh platform; intertidal.