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Mycotoxin-producing Aspergilli (<i>Circumdati</i>, <i>Flavi,</i> and <i>Nigri</i>), usually associated with contaminated food, may also cause respiratory disorders and are insufficiently studied in water-damaged indoor environments. Airborne (<i>N</i> = 71) and dust borne (<i>N</i> = 76) Aspergilli collected at post-flood and control locations in Croatia resulted in eleven different species based on their calmodulin marker: <i>A. ochraceus</i>, <i>A. ostianus</i>, <i>A. pallidofulvus, A. sclerotiorum,</i> and <i>A. westerdijkiae</i> (<i>Circumdati</i>); <i>A. flavus</i> (<i>Flavi</i>); and <i>A. tubingensis</i>, <i>A. welwitschiae</i>, <i>A. niger</i>, <i>A. piperis,</i> and <i>A. uvarum</i> (<i>Nigri</i>). Most of the airborne (73%) and dust borne (54%) isolates were found at post-flood locations, and the highest concentrations measured in indoor air (5720 colony-forming units (CFU)/m³) and dust (2.5 × 10⁵ CFU/g) were up to twenty times higher than in the control locations. <i>A. flavus</i> dominated among airborne isolates (25%) at the unrepaired locations, while 56% of the dust borne Aspergilli were identified as <i>A. tubingensis</i> and <i>A. welwitschiae</i>. The ability of identified isolates to produce mycotoxins aflatoxin B₁ (AFB₁), fumonisin B₂ (FB₂), and ochratoxin A were assessed by LC-MS analysis. All ochratoxin A (OTA)-producing <i>Circumdati</i> belonged to <i>A. westerdijkiae</i> (13.7 ± 15.81 µg/mL); in the section, <i>Flavi</i><i>A. flavus</i> produced AFB₁ (2.51 ± 5.31 µg/mL), while <i>A. welwitschiae</i> and <i>A. niger</i> (section <i>Nigri</i>) produced FB₂ (6.76 ± 13.51 µg/mL and 11.24 ± 18.30 µg/mL, respectively). Water damage dominantly supported the occurrence of aflatoxigenic <i>A. flavus</i> in indoor environments. Yet unresolved, the causal relationship of exposure to indoor Aspergilli and adverse health effects may support the significance of this research.