How to Deep Clean an Enclosure (Safe, Thorough, Species-Smart)

Use this step-by-step to fully sanitize a habitat without exposing your animal to chemical residues or temperature stress. It covers prep, disassembly, washing, disinfection with correct contact times, safe rinsing/drying, and reassembly.

1) Prep & safety

  1. Secure the animal in a temporary, escape-proof holding tub with a hide, paper towel substrate, and the correct temperature (use a heat mat or room heater if needed). Keep out of fumes and drafts.
  2. Turn off & unplug all heat/UVB/filters/pumps. Remove probe tips and label their locations.
  3. Ventilate the workspace (window/fan). Wear nitrile gloves and, if using bleach, a simple splash mask/eye protection.
  4. Never mix chemicals. Do not combine bleach with acids/ammonia. Use one disinfectant at a time on soap-free, rinsed surfaces.

2) Disassemble & remove waste

  1. Remove all décor, hides, bowls, and electronics. Keep electrical items dry (wipe-only later).
  2. Bag & discard loose substrate. For bioactive, see the notes below—deep cleaning is different.
  3. Scrape stuck debris (razor/scraper on glass only). Bin all disposable liners/papers.

3) Wash surfaces & décor (soap stage)

  1. Hot water + mild dish soap wash of the empty enclosure interior, lids, and all non-porous décor. Use separate brushes for bowls vs. tank.
  2. Rinse thoroughly until there’s no suds. Soap must be gone before disinfection.
  3. Porous wood/cork: shake off debris, then pour boiling water over pieces in a sink/tub and let stand until cool. If heavily soiled, replace rather than risk harboring pathogens.

4) Disinfect (choose one method; observe contact time)

DisinfectantWorking dilutionContact timeUse on
Bleach (sodium hypochlorite ~6%) 1:32 (½ cup per 1 gal / 120 mL per 3.8 L) 10 minutes Glass, plastic, ceramic, sealed surfaces. Not on metal finishes or porous décor.
Chlorhexidine 0.05% working solution 5–10 minutes Glass/plastic/ceramic and most tools; gentle odor; avoid direct contact with eyes.
70% Isopropyl alcohol Ready to use At least 1 minute wet (small parts) Small non-porous parts, probes (power off). Flammable; ventilate; not for large areas.
  1. Saturate surfaces evenly (spray or wipe so they stay visibly wet) and start a timer for the listed contact time.
  2. For bowls and hides: submerge in a labeled basin of your chosen disinfectant for the full contact time.
  3. Keep pets/children away while disinfectant is on surfaces.

5) Rinse, dry, off-gas before use

  1. Rinse thoroughly with clean water after the contact time. For amphibians or very sensitive species, finish with a dechlorinated or distilled water rinse on bowls and high-contact areas.
  2. Air-dry completely. Prop doors/lids open; run a small fan across the opening. No residual odor should remain.
  3. Wipe electronics & cords with a disinfectant wipe (power off), then a damp cloth to remove residue; dry fully.

6) Rebuild & reheat (verify parameters before reintroduction)

  1. Place heavy décor directly on the tank floor (glass/liner) and build substrate around it to prevent shifting.
  2. Add fresh substrate/liners. Install clean bowls and hides.
  3. Reinstall heat/UVB. Run the enclosure empty for 30–60 minutes to re-establish temperatures/UVB and ensure no chemical odor remains.
  4. Verify basking surface, warm-side/cool-side ambients, and humidity. Then return the animal.

7) How often to deep clean

  • Simple setups (paper/loose substrate): spot-clean daily; deep clean bowls weekly; full deep clean every 4–6 weeks or sooner if soiled/odor.
  • Bioactive: do not routinely strip; instead, deep clean bowls weekly, spot clean daily, and only perform full disinfection if there is a health issue (see notes).
  • Quarantine/ill animals: increase frequency (weekly full disinfection; daily bowl disinfection).

8) Special notes

Bioactive enclosures

  • Remove uneaten food and waste promptly; top up leaf litter; rake high-traffic areas.
  • If you suspect parasites or contagious disease: isolate the animal, remove and discard substrate, disinfect hardscape/enclosure as above, and reset the bioactive after veterinary guidance.

Amphibians & very sensitive species

  • Prefer low-odor disinfectants (e.g., chlorhexidine). Rinse thoroughly and finish with dechlorinated water.
  • Allow extra dry time and ensure zero residual smell before reintroduction.

Mites or heavy contamination

  • Discard porous décor and substrate. For non-porous items, complete the full disinfect cycle.
  • Between stages, keep the animal in a simple paper-lined tub and follow a targeted parasite treatment plan as directed by a vet.

Water bowls & food dishes

  • Daily: hot soapy wash → rinse → quick disinfect (per table) → final rinse → dry.
  • Avoid scented detergents; no dishwasher “rinse aids” that leave residue.