PLGA (poly(lactic-co-glycolic acid))-based nanoparticles (NPs) are promising drug carrier systems because of their excellent biocompatibility and ability for sustained drug release. However, it is not well understood how the kinetics of such drug delivery system perform in the retinal blood circulation as imaged in vivo and in real time. To answer this question, PLGA NPs were loaded either with lipophilic carbocyanine perchlorate (DiI) or hydrophilic Rhodamine 123 (Rho123) and coated with poloxamer 188 (P188): PLGA-DiI/P188 and PLGA-Rho123/P188. All particles had narrow size distributions around 130 nm, spherical shape and negative potential. Subsequently, we performed in vivo real-time imaging of retinal blood vessels, combined with ex vivo microscopy to monitor the kinetics and to detect location of those two fluorescent markers. We found that DiI signals were long lasting, detectable >90 min in blood vessels after intravenous injection as visible by homogeneous labelling of the vessel wall as well as by spots in the lumen of blood vessels. In contrast, Rho123 signals mostly disappeared after 15 min post intravenous injection in such compartment. To explore how PLGA NP-loaded cargoes are released in the retina in vivo, we thereafter monitored the Cyanine5.5 amine (Cy5.5) covalently linked PLGA polymer (Cy5.5-PLGA) in parallel to DiI and Rho123. The Cy5.5 signal from PLGA polymer was detectable in the retina vessels >90 min for both, the Cy5.5-PLGA-DiI/P188 and Cy5.5-PLGA-Rho123/P188 groups. Microscopy of the ex vivo retina tissue revealed partial level of colocalization of PLGA with DiI but no colocalization between PLGA and Rho123 at 2 h post injection. This indicates that at least a fraction of the lipophilic DiI was preserved within NPs, whereas no hydrophilic Rho123 was associated with NPs at that time point. In conclusion, the properties of PLGA carrier-cargo system in the blood circulation of the retina might be strongly influenced by the combination of factors, including the individual properties of loaded compounds and blood milieu. Thus, it is unlikely that a single nanoparticle formulation will be identified that is universally effective for the delivery of different compounds.