While increasing atmospheric carbon dioxide (CO2) concentration alters global water chemistry (Ocean Acidification; OA), the degree of changes vary on local and regional spatial scales. Inshore fringing coral reefs of the Great Barrier Reef (GBR) are subjected to a variety of local pressures, and some sites may already be marginal habitats for corals. The spatial and temporal variation in directly measured parameters: Total Alkalinity (TA) and dissolved inorganic carbon (DIC) concentration, and derived parameters: partial pressure of CO2 (pCO2); pH and aragonite saturation state (Ωar) were measured at 14 inshore reefs over a two year period in the GBR region. Total Alkalinity varied between 2069 and 2364 µmol kg-1 and DIC concentrations ranged from 1846 to 2099 µmol kg-1. This resulted in pCO2 concentrations from 340 to 554 µatm, with higher values during the wet seasons and pCO2 on inshore reefs distinctly above atmospheric values. However, due to temperature effects, Ωar was not further reduced in the wet season. Aragonite saturation on inshore reefs was consistently lower and pCO2 higher than on GBR reefs further offshore. Thermodynamic effects contribute to this, and anthropogenic runoff may also contribute by altering productivity (P), respiration (R) and P/R ratios. Compared to surveys 18 and 30 years ago, pCO2 on GBR mid- and outer-shelf reefs has risen at the same rate as atmospheric values (∼1.7 µatm yr-1) over 30 years. By contrast, values on inshore reefs have increased at 2.5 to 3 times higher rates. Thus, pCO2 levels on inshore reefs have disproportionately increased compared to atmospheric levels. Our study suggests that inshore GBR reefs are more vulnerable to OA and have less buffering capacity compared to offshore reefs. This may be caused by anthropogenically induced trophic changes in the water column and benthos of inshore reefs subjected to land runoff.