We derive a three-dimensional theory of self-propelled particle swarming in a viscous fluid environment. Our model predicts emergent collective behavior that depends critically on fluid opacity, mechanism of self-propulsion, and type of particle-particle interaction. In "clear fluids" swimmers have full knowledge of their surroundings and can adjust their velocities with respect to the lab frame, while in "opaque fluids" they control their velocities only in relation to the local fluid flow. We also show that "social" interactions that affect only a particle's propensity to swim towards or away from neighbors induces a flow field that is qualitatively different from the long-ranged flow fields generated by direct "physical" interactions. The latter can be short-ranged but lead to much longer-ranged fluid-mediated hydrodynamic forces, effectively amplifying the range over which particles interact. These different fluid flows conspire to profoundly affect swarm morphology, kinetically stabilizing or destabilizing swarm configurations that would arise in the absence of fluid. Depending upon the overall interaction potential, the mechanism of swimming ( e.g., pushers or pullers), and the degree of fluid opaqueness, we discover a number of new collective three-dimensional patterns including flocks with prolate or oblate shapes, recirculating pelotonlike structures, and jetlike fluid flows that entrain particles mediating their escape from the center of mill-like structures. Our results reveal how the interplay among general physical elements influence fluid-mediated interactions and the self-organization, mobility, and stability of new three-dimensional swarms and suggest how they might be used to kinetically control their collective behavior. DOI: 10.1103/PhysRevE.93.043112 The collective behavior of self-propelled agents in natural and artificial systems has been extensively studied . Many of the lessons learned from experimental and theoretical work conducted on organisms as diverse as bacteria, ants, locusts, and birds [23][24][25][26][27][28][29][30][31][32][33][34][35][36] have been successfully applied to engineered robotic systems to help frame decentralized control strategies through ad hoc algorithms [37][38][39][40][41][42][43][44]. In most mathematical "swarming" models, particles are assumed to be self-driven by internal mechanisms that impart a characteristic speed. A pairwise short-ranged repulsion and a long-ranged decaying attraction are typically employed as the most realistic choices when modeling aggregating particles [9,11,45]. The interplay between self-propulsion, particle interactions, initial conditions, and number of particles is key in determining the large scale patterns that dynamically arise. In two dimensions, rotating mills and translating flocks are often observed, the latter configuration also arising in three dimensions [9,10,17,19,46,47]. It is possible to classify swarm morphology in terms of interaction strength and length scales, as shown for particles coupled via conserved f...