Cyanobacteria are key photosynthetic organisms in many aquatic ecosystems and hold great potential for sustainable green biotechnology. Growth of cyanobacteria in batch cultures is expected to be part of future biotechnological practices. However, the issue of correlating the dynamics of metabolic and photosynthetic parameters with the culture fitness during batch cultivation is still outstanding. In this paper we take advantage of a photobioreactor system to continuously track growth parameters of Synechocystis sp. PCC 6803, and to couple online culture monitoring with offline measurements of photosynthetic efficiency and biochemical and elemental cell composition under several light intensity and CO2 regimes. Light intensity determines the flux of energy into the photosynthetic system while CO2 concentrations determines the ability to capture this energy in chemical form. From this perspective, four distinct source-sink regimes were established and compared, which allowed us to reveal specific strategies to acclimate to both carbon and light limitation. As part of the measurements, room temperature excitation-emission spectra and elemental composition of Synechocystis cells were, for the first time, compared throughout the exponential and linear growth phases. In total, 39 parameters (out of 170 measured) were identified as highly correlating (R2 > 0.9) with growth rate or productivity under at least one tested cultivation condition, including concentrations and ratios of pigments or particular elements. For online fitness and productivity monitoring in cyanobacteria batch cultures, parameters such as photosynthesis and respiration rates and ratios, energy-dependent non-photochemical quenching (qE) or Zn and Mo concentration in the cultivation medium can be of interest.