Photosynthesis Equation The equation for photosynthesis is $\ce{6CO2 + 6H2O + Energy -> C6H12O6 + 6O2}$ My confusion rests in the following: during the photolysis (water-splitting) step of the light reactions that occur in Photosystem II, water gets split into 2 H+ ions, 2 electrons (which enter the photosystem), and **one** Oxygen ion. But if Oxygen ($O_2$) is comprised of **two** oxygen ions covalently bonded to each other, doesn't this mean that $\ce{6H2O -> 3O2}$ ? Could someone please clarify this for me?

Equation you have mentioned is balanced chemical equation. In reality these are series of Redox reactions, major two as follows,

Oxidation of oxygen from water in presence of light (energy from photon),

$ 2H_2O \xrightarrow{Photons} O_2 + 4H^*$

Ions produced from above reaction reduces carbon dioxide ,

$4H^* + CO_2 \rightarrow (CH_2O) + H_2O$

So both equations combined, we can write general form as

$nCO_2 + nH_2O \xrightarrow{Photons} (CH_2O)n + nO_2$

In simple words to answer your doubt, in final equation 2 oxygen molecule coming from per 2 $H_2O$ molecules and 1 coming from per $CO_2$ molecule. Hence final balanced equation is

$6CO_2 + 6H_2O \xrightarrow{Photons} 6(CH_2O) + 6O_2$