There can be interactive physical and/or chemical effects between drivers, prior to any biological effects. So care must be taken in designing experiments to take into account any physico-chemical interactions.  In studies using multiple trophic levels there can also be confounding effects, such as the different influence of multiple drivers on prey and predators.

Useful references

Boyd, P.W. Boyd and C.J. Brown (2015)
Modes of interactions between environmental drivers and marine biota. Front. Mar. Sci., https://doi.org/10.3389/fmars.2015.00009

Vinebrooke, R. D., et al. (2004).
Impacts of multiple stressors on biodiversity and ecosystem functioning: the role of species co-tolerance. Oikos 104, 451–457. doi: 10.1111/j.0030-1299.2004.13255.x

Summary of the range of permutations associated with interlinked different modes of interactions, illustrated in (A) for iron supply for phytoplankton (note brown arrow in right hand panel denotes changes in foodweb interactions driven by floristic and consequent faunistic shifts; see main text for details); (B) provides examples of physicochemical interactions, and how top-down ecological effects will interact across these modes of interactions. From Boyd & Brown (2015).