Like most commodities, coffee’s worst enemy is the weather. Many coffee producers are going to struggle through the rest of this year and much of 2015 under the combined impact of a strong El Niño and “la roya.” But a bad year for coffee could be a good year for investors.

The quality and quantity of the coffee harvest closely tracks the cycle of El Niño and La Niña weather patterns. La Niña years, and for a period of time after, mark a time of abundance and lower prices. During El Niño years, and for a short period of time after, the crop is poor and prices jump.

Tropical weather patterns began to shift late last year ahead of El Niño. Four of the top five coffee producing nations are in a drought and the fifth will face it late this summer. In fact, coffee prices have climbed sharply since early January as it became clear that drought had ravaged Brazilian coffee. The coffee crop from Brazil is expected to fall 20%. The situation doesn’t look much better for the other major coffee-growing countries. Indonesia has been suffering through a drought, while drought conditions have just started to settle in for Colombia and Vietnam.

Ethiopia, the world’s fifth largest grower, has been profiting from Brazil’s woes because their weather has been great for growing coffee. But their fortune will change in August, as El Niño reduces their rainfall to about half of normal.

And then there’s “la roya.”

Central America accounts for about 9% of the world’s supply of coffee. The weather has been hot, allowing “la roya,” or coffee rust, to spread. Coffee rust is a fungus that infests the leaves of the coffee plant. The fungus spreads quickly in the hot weather, withering trees and sharply slashing production. The weapons of choice to battle coffee rust: spraying coffee plants with fungicide and cooler temperatures. Spraying costs money — money that small growers don’t have or are forced to borrow. The alternative — cooler temperatures — will arrive in August as part of the El Niño cycle. Even so, it will take months to years for coffee plants to recover.

Rain will return to Brazil in July just as Colombia and Central America dive deep into drought. Brazil’s rain usually comes back with a vengeance, increasing the risk for flooding and landslides, which will cause even more damage to the coffee plants.

Coffee will be in short supply for another two years before the weather becomes favorable again.

Making a profitable investment in coffee requires careful research and discipline. There are a variety of ways that you can invest in coffee, but there are few pure plays that will allow you to pocket a nice gain. Chasing coffee shops can be a trip down the rabbit hole because there are so many other variables in that space and coffee is a high-margin item. A cup of $2 coffee only costs about 40 cents to make. That includes the cup, lid, cardboard sleeve and the coffee.

The largest players, Starbucks (NASDAQ: SBUX) and Dunkin Brands Group (NASDAQ: DNKN), for example, leverage long-term contracts for coffee. Starbucks has its 2014 supply and 40% of its fiscal 2015 supply under contract, locking in a price so that it isn’t vulnerable to market fluctuations. Dunkin has coffee contracted through the end of the year. You won’t see the price of coffee increase at Dunkin until the fourth quarter, according to its latest analyst’s call.

I like to trade coffee through a smaller roaster who passes the cost along to their large customers. You have to do some research to make sure the roaster's stock reacts to the price of coffee so you know you have more of pure play. But use caution, because once the price of coffee starts to go down you'll need to react quickly to lock in your gains.