Toyota Camry 1994: Dark brown coolant

Three months ago I had to replace a cracked radiator in my 1994 V6 Toyota Camry. We found that the water was dark brown there was sediment two centimetres thick in the reservoir. My mechanic told me to flush the system with clean water every week until no more dirt was coming out and then put coolant in it and leave it, and that's what I did. Two weeks later I began to have problems starting the engine, and was running roughly and there was a lot of steam coming out of the exhaust. This time the mechanic told me to flush the water and put Chemiweld on for two weeks without coolant, then flush it out and replace it with fresh coolant. After doing that the engine is no running roughly and there is also less steam coming out from the exhaust, but the water is continuously coming out dirty and forms settlement in the plastic reservoir. What do you think the problem could be?