"can substantially affect" is correct and usable in written English.
You can use it when describing how one thing can have an important impact on another. For example, "The use of technology in the classroom can substantially affect student learning."
The point is that the strength of these ties can substantially affect interactions, outcomes and well-being.
This lapsed time can substantially affect the strength and ductility of the material.
Hypofunction of the salivary glands can substantially affect quality of life.
Thus, biodiesel tends to have variable fuel properties that can substantially affect engine performance (Fortman et al. 2008).
Even a small difference in the catalyst performance can substantially affect the bottom line of a refinery.
Cognitive impairments are highly prevalent in stroke survivors and can substantially affect their physical rehabilitation and quality of life.
Surface treatment of different steels and metal alloys in such a dense plasma environment can substantially affect the surface profile.
The feed force applied in the grinding process can substantially affect the grinding contact stiffness; as a result, it can significantly influence the resonance.
The analysis showed that both measurement methodology and core diameter can substantially affect the specific gravity determination and, as a consequence, the air void content estimate.
Importantly, the method used to define EJ communities can substantially affect the analytical outcome, potentially shifting a finding of inequity from null to positive or vice versa.
Charge variants, which are among the most important quality attributes, can substantially affect the in vitro and in vivo properties of mAbs.
