High initial cost - The initial investment and maintenance cost for a micro irrigation system maybe higher than for some other irrigation methods, but the growers should weight the cost against benefits. Filters, pumps, regulators, valves, gauges, chemical injectors and possible automation components add to the cost of a micro irrigation system. The emitter itself (drip tube/tape, sprayer, sprinkler) represents only approximately 35 - 37% of the initial system cost. Actual cost will vary considerably depending on the selection of a particular micro system. The growers must understand that a well designed, installed and managed system has water saving and important agronomic, environment and economic benefits.

Requires some management and maintenance - Farming with micro irrigation systems typically requires a change in cultivation, planting and harvesting practises. Educating growers of these changes is required before and during the first season of the micro irrigation. These new practises can quickly become a standard part of the farming operation. Micro irrigation systems normally have greater maintenance because of the small orifice characteristics which are susceptible to clogging from particulate matters, organic matter, and chemical precipitates. Therefore additional maintenance - including filtration, injecting chlorine or acid and flushing lateral lines -  maybe necessary to ensure top performance. Machinery, animals, insects or food traffic in the field can cause leaks in the drip tape. Also in order to realise the many benefits discussed, the grower must constantly be monitoring the growing environment and scheduling irrigation to meet the plant's needs.  Fragment inspections of drip systems are recommended and the timely corrections of problems is critical to not risk stressing a crop.

Clogging - One of the biggest problems encountered under micro irrigation is clogging of emitters. The small openings can be easily clogged by soil particles, organic matter, bacterial slime, algae or chemical precipitates. The micro irrigation system requires very good filtration (most often recommended 200 mesh filtration degree) even with a good quality water supply. The filtration system should be chosen based on physical, chemical or biological characteristics of the water.

Salt accumulation near the root zone - Unlike surface and sprinkler irrigation systems, which can flush salts below the crop root zone, micro irrigation systems tend to move salts to the outer edge of the wetted volume of soil and soil surface. Insufficient rainfall can move the salts back into the root zone and cause damage. Careful management is necessary to ensure that the salts do not migrate back into the active root zone. If the need to leach salts from the root zone becomes critical a sprinkler or surface irrigation system may have to be used to accomplish this purpose effectively. In areas, with heavy rainfall the salts will be washed out of the root zone before significant accumulation occurs.

Seed germination - Some crops do not germinate well with micro irrigation systems (usually under drip tube/tape). In these cases portable sprinklers are often used for germination. Once started the crop can be irrigated with micro irrigation to optimise plant growth. 

Moisture distribution/restricted root zone - Moisture distribution depends largely on the soil type being irrigated by the micro irrigation system. In some soils, i.e. deep sands, very little lateral water movement (low capillary forces) can create many problems. Under these conditions it is difficult to wet a significant portion of the root zone. It is also more difficult to manage the irrigation without deep percolation since only a small amount of water can be stored in the wetted volume desired. Increasing the number of emitters per plant may improve water distribution in the soil. Therefore, coarse sands will require much closer spacing of emitters than fine soils. In general, for any soil the amount of emitters and their spacing must be based on the geometry of wetted soil volume. Particularly in regions of low rainfall, plant root activity is often limited to the soil zone wetted by the emitters.  The irrigator must remember that the micro irrigation system is meant to apply small, frequent irrigations.