Green Algae vs Brown Algae in New Tank: Complete Timeline & What to Do

If you’re seeing brown algae in your new tank right now and Googling “is this normal?” – YES, it’s 100% normal. But here’s what most guides won’t tell you: brown algae is just Phase 1 of a predictable algae succession timeline that every new tank goes through. Understanding what comes next (spoiler: green algae in weeks 4-8) and how to manage the transition is the difference between a smooth setup experience and months of frustration.

This guide will show you the complete brown-to-green algae timeline, explain WHY each algae type appears when it does, and give you a 3-stage management strategy so you know exactly what to do (and what NOT to do) at each phase of your new tank’s maturation.

Brown Algae vs Green Algae: The Complete Comparison

Before we dive into the timeline, let’s compare these two algae types side-by-side so you can identify which one(s) you’re dealing with:

The New Tank Algae Timeline: What to Expect Week-by-Week

Understanding WHEN each algae type appears helps you anticipate what’s coming and avoid panic reactions. Here’s the predictable progression every new tank follows:

Week 1-2: The Brown Algae Arrival 🟤

What You’ll See:

• Fine brown/tan dusty coating starts appearing on glass (usually back/side walls first)
• Substrate develops brownish tint (especially white sand or light gravel)
• Plant leaves get light brown film
• Decorations and rocks show dusty brown patches

What’s Happening: Your new substrate, decorations, and glass are releasing silicates (silicon dioxide) into the water. Diatoms (brown algae) feast on these silicates. This is a NORMAL part of the nitrogen cycle starting.

What to Do:

• ✅ WIPE front glass 1-2x weekly (for viewing only – don’t scrub the whole tank)
• ✅ CONTINUE normal cycling process (test ammonia/nitrite, don’t add fish yet if fishless cycling)
• ✅ CONSIDER adding 6+ Otocinclus catfish IF you’re doing fish-in cycling and tank has been running 3+ weeks
• ❌ DO NOT use algae remover chemicals (kills beneficial bacteria, delays cycling)
• ❌ DO NOT do large water changes (>50%) trying to “wash out” the algae (disrupts cycling)
• ❌ DO NOT scrub decorations daily (waste of time – algae returns in 24-48 hours)

Week 3-4: Peak Brown Algae (The “Ugly Stage”) 🟤🟤🟤

What You’ll See:

• Brown algae coating becomes THICK and highly visible everywhere
• Front glass needs wiping every 2-3 days to see fish clearly
• Plants may look completely brown (can’t see green leaves underneath)
• Tank looks like a “dust storm” – this is the worst it will look

What’s Happening: Silicate levels peak as all surfaces continue releasing silicon. Your nitrogen cycle is mid-process (ammonia dropping, nitrite spiking). Diatoms are thriving in these conditions.

What to Do:

• ✅ STAY THE COURSE – this is peak ugliness, but it’s temporary (1-2 weeks)
• ✅ TEST water parameters weekly (ammonia should be dropping, nitrite rising, then falling)
• ✅ ADD Otocinclus catfish NOW if you haven’t already (they’ll clear 70-80% of brown algae in 5-7 days)
• ✅ WIPE front glass as needed for viewing
• ❌ DO NOT restart your tank (biggest mistake beginners make – this phase ALWAYS happens)
• ❌ DO NOT reduce lighting below 6 hours thinking it will help brown algae (doesn’t affect diatoms – they don’t need much light)

Week 5-6: Brown Algae Starts Clearing 🟤→🟢

What You’ll See:

• Brown algae noticeably thinner on glass and decorations
• Can start seeing plant leaves’ true green color again
• Front glass stays cleaner for 5-7 days between wipes (vs. 2-3 days before)
• First hints of green algae may appear (light green film on front glass, small green dots)

What’s Happening: Silicates are depleting as surfaces stop releasing them. Your nitrogen cycle is completing (ammonia 0, nitrite dropping to 0, nitrates rising to 5-20ppm). Diatoms are starving without silicates. Green algae starts colonizing as light + nutrients are now available.

What to Do:

• ✅ INSTALL LIGHT TIMER NOW (set to 6-8 hours max) – CRITICAL for preventing green algae explosion
• ✅ START 20% weekly water changes (tank should be cycled or nearly cycled by now)
• ✅ TEST nitrates – if >20ppm, increase water changes to 30% twice weekly
• ✅ ADD fast-growing live plants (Hornwort, Water Sprite, Guppy Grass) – they’ll compete with green algae for nutrients
• ✅ CONTINUE wiping front glass as needed
• ❌ DO NOT increase lighting duration thinking “more light = less algae” (OPPOSITE is true for green algae)

Week 7-8: Brown Algae Gone, Green Algae Prevention Mode 🟢

What You’ll See:

• Brown algae 90-95% gone (maybe trace amounts in low-flow corners)
• Tank water crystal clear
• Light green film on front glass (manageable with weekly wipe)
• Small green dots may appear on back/side glass (green spot algae – normal)

What’s Happening: Your tank is now “matured.” Nitrogen cycle complete (ammonia 0, nitrite 0, nitrates 5-20ppm). Beneficial bacteria established. Green algae is now the primary algae type trying to colonize.

What to Do:

• ✅ MAINTAIN strict lighting schedule (6-8 hours daily, NO EXCEPTIONS – this is your #1 green algae prevention)
• ✅ FEED fish conservatively – only what they eat in 2 minutes, once daily (overfeeding fuels green algae)
• ✅ CONTINUE 20-30% weekly water changes (removes nitrates before green algae can use them)
• ✅ KEEP algae-eating crew (Otocinclus, Nerite snails) – they prevent green algae from establishing
• ✅ WIPE front glass 1x weekly (takes 2 minutes with magnetic cleaner)
• ❌ DO NOT skip water changes “just this once” (green algae explodes within 2 weeks if nitrates climb)

Week 9+ (Month 3+): Fully Established Tank 🟢✅

What You’ll See:

• Light green film on glass (5-10% coverage) – NORMAL and healthy
• Trace green algae on decorations – ignorable
• Tank looks clean with minimal effort

What’s Happening: Your tank ecosystem is balanced. Algae exists but at manageable levels (under 10% coverage). This is the goal state.

Ongoing Maintenance:

• Light timer: 6-8 hours daily
• Feeding: Once daily, conservative portions
• Water changes: 20-30% weekly
• Glass wipe: 1x weekly (2 minutes)
• Nitrate testing: Monthly (target <20ppm)

The 3-Stage Management Strategy (What to Do at Each Phase)

Now that you understand the timeline, here’s your action plan for each stage:

Stage 1: Brown Algae Phase (Week 1-4) – “Wait It Out”

Stage 2: Transition Period (Week 4-8) – “Prevention Setup”

Stage 3: Green Algae Prevention (Week 8+) – “Maintain Discipline”

5 Real Case Studies: Different Tanks, Same Timeline

Decision Tree: Should I Do Something About This Algae?

Use this flowchart to decide if action is needed:

Common Questions: Brown Algae vs Green Algae

Final Thoughts: Embracing the Timeline

After 8 years of setting up tanks (12 tanks total, ranging from 5G to 75G), I can tell you with 100% certainty: Every single new tank goes through the brown algae phase. High-tech, low-tech, planted, non-planted, expensive, budget – doesn’t matter. Brown algae appears in weeks 1-4, peaks around week 3-4, then clears by week 6-8. It’s as predictable as the nitrogen cycle itself.

The difference between beginners who panic (spending $50-100 on useless chemicals, restarting tanks, endless scrubbing) and experienced hobbyists (who calmly wait 4-6 weeks) is simple: understanding the timeline.

Once you know that brown algae is temporary and self-resolving, you stop fighting it. Once you know that green algae appears during the transition period (weeks 4-8), you set up prevention BEFORE it explodes. And once you establish the Stage 3 maintenance routine (light timer, feeding discipline, weekly water changes), algae becomes a non-issue – just 2 minutes of glass wiping weekly.

Here’s what I want you to remember:

• ✅ Brown algae = normal new tank phase (weeks 1-6). Don’t panic. Wait it out or add Otocinclus.
• ✅ Green algae = mature tank challenge (weeks 4+). Requires prevention setup (light timer, feeding discipline, water changes).
• ✅ Week 5-6 is THE critical decision point. Install light timer and add plants NOW = easy green algae control. Do nothing = green algae nightmare by week 10.
• ✅ Don’t restart your tank because of brown algae. You’ll get it again in the new setup. Just wait 4-6 weeks.
• ✅ Chemicals don’t work for brown algae (kills beneficial bacteria, delays cycling). Otocinclus work better, faster, and cheaper long-term.

Your tank will mature. The brown algae will clear. If you set up green algae prevention during the transition, your tank will look stunning by month 3 with minimal maintenance. Trust the timeline.